| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:28 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the GenomicFeatures package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 716/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicFeatures 1.42.3 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicFeatures |
| Version: 1.42.3 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicFeatures_1.42.3.tar.gz |
| StartedAt: 2021-05-06 03:05:58 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:40:29 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 2071.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicFeatures.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GenomicFeatures_1.42.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicFeatures.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.42.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicFeatures' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:100: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:54: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:58: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:62: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:26: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:27: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:28: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:32: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:33: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:35: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:38: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:43: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:70: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:71: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:75: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:80: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:102: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:108: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/disjointExons.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:38: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:44: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:91: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:102: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:141: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:44: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:46: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:79: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:84: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:87: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:93: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:103: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:132: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractTranscriptSeqs.Rd:135: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:109: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:117: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDb.Rd:201: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDb.Rd:206: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDb.Rd:207: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromBiomart.Rd:144: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:80: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: file link 'GFF3File' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: file link 'GTFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGFF.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:51: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:52: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:121: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/mapRangesToIds.Rd:25: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLengths.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLengths.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:84: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:93: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:126: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:52: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:54: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicFeatures.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeTxDbFromBiomart 94.86 1.86 195.42
makeFeatureDbFromUCSC 38.43 9.49 126.31
exonicParts 44.91 2.74 47.64
coverageByTranscript 28.25 4.11 32.37
makeTxDbFromUCSC 17.09 0.34 62.66
makeTxDbFromGFF 13.20 0.00 13.41
extractTranscriptSeqs 12.45 0.25 12.71
transcriptLocs2refLocs 11.31 1.10 19.33
coordinate-mapping-methods 11.12 0.39 96.64
transcriptLengths 5.38 0.09 5.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeTxDbFromBiomart 57.14 1.51 118.50
coordinate-mapping-methods 53.24 2.27 61.19
exonicParts 48.88 2.00 50.88
makeFeatureDbFromUCSC 36.99 1.11 107.99
coverageByTranscript 21.57 4.37 25.95
makeTxDbFromUCSC 15.57 0.27 67.53
extractTranscriptSeqs 14.41 0.44 14.84
transcriptLocs2refLocs 10.50 0.89 11.89
makeTxDbFromGFF 8.62 0.05 8.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.
GenomicFeatures.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicFeatures_1.42.3.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.42.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.42.3.zip && rm GenomicFeatures_1.42.3.tar.gz GenomicFeatures_1.42.3.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1134k 100 1134k 0 0 42.5M 0 --:--:-- --:--:-- --:--:-- 44.3M
install for i386
* installing *source* package 'GenomicFeatures' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicFeatures'
finding HTML links ... done
FeatureDb-class html
finding level-2 HTML links ... done
TxDb-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:100: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
as-format-methods html
coordinate-mapping-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:54: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:58: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:62: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
coverageByTranscript html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:26: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:27: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:28: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:32: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:33: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:35: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:38: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:43: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:70: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:71: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:75: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:80: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:102: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:108: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
disjointExons html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/disjointExons.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
exonicParts html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:38: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:44: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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extractTranscriptSeqs html
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extractUpstreamSeqs html
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features html
getPromoterSeq-methods html
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id2name html
makeFeatureDbFromUCSC html
makeTxDb html
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makeTxDbFromBiomart html
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makeTxDbFromEnsembl html
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makeTxDbFromGFF html
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makeTxDbFromGRanges html
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
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makeTxDbFromUCSC html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:51: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:52: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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makeTxDbPackage html
mapIdsToRanges html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
mapRangesToIds html
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microRNAs html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
nearest-methods html
select-methods html
transcriptLengths html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLengths.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLengths.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
transcriptLocs2refLocs html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
transcripts html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:84: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:93: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:126: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
transcriptsBy html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:54: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsBy.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
transcriptsByOverlaps html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.42.3.zip
* DONE (GenomicFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked
|
GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
RUNIT TEST PROTOCOL -- Thu May 06 03:36:20 2021
***********************************************
Number of test functions: 73
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73
Number of errors: 0
Number of failures: 0
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 3 out-of-bound ranges located on sequences a,
b, and c. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 4 out-of-bound ranges located on sequences 1,
2, 3, and 4. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?`trim,GenomicRanges-method` for more information.
5: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
exon. This information was ignored.
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
7: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
>
> proc.time()
user system elapsed
228.40 14.06 321.00
|
GenomicFeatures.Rcheck/tests_x64/run_unitTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
RUNIT TEST PROTOCOL -- Thu May 06 03:40:18 2021
***********************************************
Number of test functions: 73
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73
Number of errors: 0
Number of failures: 0
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 3 out-of-bound ranges located on sequences a,
b, and c. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence c.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 4 out-of-bound ranges located on sequences 1,
2, 3, and 4. Note that ranges located on a sequence whose length is
unknown (NA) or on a circular sequence are not considered out-of-bound
(use seqlengths() and isCircular() to get the lengths and circularity
flags of the underlying sequences). You can use trim() to trim these
ranges. See ?`trim,GenomicRanges-method` for more information.
5: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
exon. This information was ignored.
6: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
7: In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
>
> proc.time()
user system elapsed
178.21 2.75 237.20
|
|
GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings
|
GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings
|